GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Pseudomonas fluorescens GW456-L13

Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate PfGW456L13_3630 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)

Query= BRENDA::C7R702
         (374 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3630
          Length = 372

 Score =  619 bits (1596), Expect = 0.0
 Identities = 296/370 (80%), Positives = 337/370 (91%)

Query: 5   VIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSI 64
           +IK +AAVA+ A +PL I EV+V PPQ GEV V+IVATGVCHTDAFTLSG DPEG+FP I
Sbjct: 1   MIKSRAAVAFAANQPLQIVEVDVAPPQAGEVLVRIVATGVCHTDAFTLSGADPEGIFPVI 60

Query: 65  LGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMP 124
           LGHEGGGIVE+VGEGVTS+  GDHVIPLYTPECG+CKFC SGKTNLCQKIR TQGKGLMP
Sbjct: 61  LGHEGGGIVEAVGEGVTSLAVGDHVIPLYTPECGECKFCTSGKTNLCQKIRATQGKGLMP 120

Query: 125 DGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVM 184
           DGT+RFS  G+P++HYMGTSTFSEYTVLPEISLAK+   APLE+VCLLGCGVTTG+GAV+
Sbjct: 121 DGTSRFSYEGQPVFHYMGTSTFSEYTVLPEISLAKIPKDAPLEKVCLLGCGVTTGIGAVI 180

Query: 185 NTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPK 244
           NTAKVEEGA+VAIFGLGGIGL+A+IGA MAKA RIIAIDIN +KFE+A++LGATD +NPK
Sbjct: 181 NTAKVEEGASVAIFGLGGIGLAAIIGATMAKAGRIIAIDINPAKFEIARQLGATDFINPK 240

Query: 245 DYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTR 304
           DYD+PIQ+VI+EMT+GGVDYSFECIGNV++MR+ALECCHKGWGESVIIGVAGAGQEISTR
Sbjct: 241 DYDRPIQDVIIEMTEGGVDYSFECIGNVHLMRAALECCHKGWGESVIIGVAGAGQEISTR 300

Query: 305 PFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHE 364
           PFQLVTGRVW+G+AFGGVKGRSELP YVE    G+  LD FITHTM LE+IN AFDLMH+
Sbjct: 301 PFQLVTGRVWRGSAFGGVKGRSELPSYVENAQKGDIPLDSFITHTMGLEEINRAFDLMHK 360

Query: 365 GKSIRSVIHY 374
           G+SIR+VIH+
Sbjct: 361 GESIRTVIHF 370


Lambda     K      H
   0.317    0.137    0.413 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 595
Number of extensions: 19
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 374
Length of database: 372
Length adjustment: 30
Effective length of query: 344
Effective length of database: 342
Effective search space:   117648
Effective search space used:   117648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory